Abstract: The study aims to investigate the effects of planting Vicia villosa green manure during winter fallow and its incorporation into soil on soil environment of tobacco fields and flue-cured tobacco quality in Lijiang, Yunnan Province. Four sowing rate treatments were established: (D1) 60 kg/hm²; (D2) 45 kg/hm²; (D3) 30 kg/hm²; and (CK) 0 kg/hm², corresponding to the incorporation rates of 7800, 6300, 3 800 kg/hm², and 0 kg/hm², respectively. Rhizosphere soil nutrients and microbial communities, as well as yield and quality of flue-cured tobacco leaves were assessed 70 days after transplantation. Results showed that the incorporation treatment of 7800 kg/hm² significantly increased soil electrical conductivity (increase of 48.83%), available nitrogen (67.41%), available phosphorus (98.61%), available potassium (104.76%), and organic matter (24.11%). Microbiome analysis revealed that the high application rates (7800 and 6300 kg/hm²) significantly enhanced the bacterial α-diversity but not fungal α-diversity. Principal coordinate analysis (PCoA) based on Bray-Curtis distances demonstrated that Vicia villosa incorporation significantly altered microbial community structure. Random forest analysis identified that the abundance of beneficial microorganisms, including Sphingobacterium, Terrimonas, Metarhizium, and Penicillium, involved in nutrient activation and disease suppression, was significantly increased. Redundancy analysis (RDA) indicated that soil physicochemical properties explained 38.09% and 37.85% of the variation in bacterial and fungal communities, respectively, with available nitrogen as the main driving factor. Co-occurrence network analysis revealed that the incorporation induced reconstruction of microbial functional modules, enriching bacterial modules that dominated nitrogen cycling, photosynthesis, and organic matter degradation, while significantly reducing the abundance of fungal modules with potential negative functions. Moreover, changes in all modules were significantly correlated with soil physicochemical properties. Agro-economic analysis showed that the application of 7800 kg/hm² dry mass (equivalent to 26441 kg/hm2 fresh mass) achieved optimal yield and output value, along with significantly enhanced appearance & sensory quality of tobacco leaves. The study confirms that green manure-driven rhizosphere micro-ecosystem reconstruction represents an effective approach to improve flue-cured tobacco quality, and Vicia villosa has promising applications in green tobacco production.